Next-Generation Prospecting in the Yukon Territory: Mining Stress Tolerance Traits using a Native Extremophile Plant

Functional genomics studies of extremophile plants growing in their natural environment afford an opportunity to identify stress tolerance genes that are regulated to maximize plant performance under physiologically challenging conditions.  We used RNA-Seq in an innovative ecological approach involving a population of Thellungiella salsuginea, a mustard native to the Canadian Yukon, to discern genes responsible for its natural adaptations to salinity and cold temperatures.  We profiled transcriptomes of plants exposed to cold temperatures and saline soil under field conditions and, in parallel, plants that were well-watered, salt or cold stressed in cabinets.  This approach is designed to test the hypothesis that traits essential for tolerance to a specific stress will be expressed regardless of the location where that stress is incurred.  Two billion cDNA sequences were obtained from 34 cDNA libraries representing plants subjected to simulated stress treatments in growth cabinets and plants found at a Yukon field site.  Multivariate statistical analyses showed that transcriptomes of plants from the field site were as reproducible as those from inbred plants grown under controlled conditions.  Furthermore, statistically significant patterns of differential gene expression could be detected from a few individuals.  From the expression profiles of 27016 annotated Thellungiella genes we identified a subset of only 26 cold and salt-responsive genes common to plants found in the field and stressed in the cabinet.   The process of virtually subtracting gene expression patterns is a valuable bioinformatics approach that can distill a small but physiologically meaningful group of co-regulated genes from large transcriptomic datasets.